MolNFT v1 · #122033 · protein
Crystal structure of equine serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cpa)
5ID9: “Crystal structure of equine serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic…”. X-ray diffraction, 1 ligand (6A4), 9 pockets (best druggability 0.79). MolNFT v1 #122033 on GenesisL1: 3D structure…
- PDB
- 5ID9
- Type
- protein
- Length
- 580 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin
- UniProt
- F7BAY6
- Ligands
- 6A4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serum albumin | protein | 580 | 74% helix, 0% strand | F7BAY6 |
Ligands and binding sites
- 6A4 · (4S)-2-sulfanylidene-4-[(tetradecanoyloxy)methyl]-1,3,2lambda~5~-dioxaphospholane-2-thiolate · ligand · chains A
- FMT · Formic acid · additive · 4 copies · chains A
- MLI · Malonate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.79 | 0.85 | 59 | MLI, FMT |
| 2 | 890 | 0.78 | 0.81 | 60 | MLI, FMT |
| 3 | 175 | 0.67 | 0.86 | 32 | empty |
| 4 | 213 | 0.62 | 0.82 | 25 | FMT |
| 5 | 230 | 0.62 | 0.81 | 27 | 6A4 |
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 5ID9 · Crystal structure of equine serum albumin in complex with phosphorodithioate derivative… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F7BAY6
- Elsewhere: RCSB PDB 5ID9 · PDBe 5ID9 · UniProt F7BAY6
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